Post on 22-Jul-2020
18th Annual Biomedical Computation atStanford Symposium
Stanford University
April 19, 2018
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2018 University Sponsors
2018 Corporate Sponsors
AncestryDNA
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BCATS Symposium ScheduleThursday April 19, 2018 | Li Ka Shing Center, Paul Berg Hall (2nd floor)For event details and a list of our 2018 sponsors, please visit: www.bcats.stanford.edu
Session 1
8:30 AM Sign-in & Breakfast
9:00 AM Opening Remarks
9:15 AM Keynote Address: Nathan Price, PhD
Institute of Systems BiologyMining personal, dense, dynamic data clouds to enhance health anddrive discovery
10:00 AM Emily Flynn
Meta-analysis of sex-differential gene expression in human liver
10:15 AM Erika Bongen
KLRD1 expressing NK cells may protect against influenza infection
10:30 AM Coffee Break
Session 2
10:45 AM Pratheepa Jeganathan
The block bootstrap method for longitudinal microbiome data
11:00 AM Boxiang Liu
Genetic regulatory mechanisms of smooth muscle cells map to coronaryartery disease risk loci
11:15 AM Keynote Address: Jason Ernst, PhD
University of California, Los AngelesComputational approaches for interpreting the epigenome and non-coding genome
12:00 PM Lunch
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Session 3
1:00 PM Keynote Address: Priya Moorjani, PhD
University of California, BerkeleyGenetic insights into South Asian population history and disease
1:45 PM Winn Haynes
Gene annotation bias impedes biomedical research
2:00 PM David Gokhman
Reconstructing Denisovan anatomy using DNA methylation maps
2:15 PM Keynote Address: Ryan Hernandez, PhD
University of California, San FranciscoHow evolutionary forces shape the genetic architecture of complextraits
3:00 PM Snack Break
Session 4
3:15 PM Industry Panel
• 3T Biosciences: Dr. Marvin Gee
• AncestryDNA: Drs. Eurie Hong, Natalie Telis
• Cardinal Analytx Solutions: Drs. Brian Maples, Joe Davis
• IBM: Dr. Ban Kawas
4:00 PM Closing Remarks
4:15 PM Poster Session & Happy Hour
Paul Berg Hall, Room A
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About Us
Yosuke Tanigawa2nd year, Biomedical Informatics
Rivas & Bejerano Labs
Yosuke is a 2nd year Ph.D. student in BiomedicalInformatics Training Program after he receivedBS in Bioinformatics and Systems Biology fromUniversity of Tokyo. He is jointly advised by Dr.Manuel Rivas and Dr. Gill Bejerano and workingon methods development for large-scale humangenetics dataset. He enjoys swimming, running,
and playing the piano.
Nicole Ferraro2nd year, Biomedical Informatics
Montgomery Lab
Nicole received a dual BS/MS in BiomedicalEngineering from Drexel University in
Philadelphia, PA in 2016. She is currently asecond year in the Stanford Biomedical
Informatics training program. As a member ofthe Montgomery Lab, Nicole works on methods
development to understand the genetic influencesunderlying gene expression, and incorporate
multi-omics data modalities to characterize theimpact of rare variation. She enjoys running,vegetarian cooking, and exploring new cities.
Irene Li2nd year, Cancer Biology
Plevritis Lab
Irene is a second-year in the Cancer Biologyprogram and received her bachelors in MolecularGenetics and Global Public Health at Michigan
State University. She investigates metabolic shiftsand progressions in the tumor microenvironmentin the Plevritis Lab. Shes an avid painter, piano
& ukulele player, and hiker.
Samantha Piekos3rd year, Stem Cell Biology & Regenerative Medicine
Oro Lab
Samantha received her BS in Biological Sciencesand Psychology from the University of Notre
Dame. Currently, she is a third year PhD studentin the Stem Cell Biology & Regenerative
Medicine and is advised by Dr. Anthony Oro.Her research focuses on understanding how thechromatin landscape changes during early skin
differentiation. In her free time, Samantha enjoysspending time outdoors whether it be hiking or
traveling. She also enjoys rock climbing and is anavid cook.
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Lawrence Bai2nd year, Immunology
Habtezion & Khatri Labs
Lawrence graduated with a BS in MicrobialBiology from UC Berkeley in 2016 before joiningthe Immunology Program at Stanford University.He is currently in his second year, where he works
on better understanding inflammatory boweldisease from a systems biology perspective. He isjointly advised by Dr. Aida Habtezion and Dr.Purvesh Khatri. In his spare time, Lawrence
enjoys going on food adventures with his friends,whether it be exploring new restaurants or
cooking at home. He also enjoys listening tomusic and traveling around the world to betterunderstand other cultures (including cuisines,
language, and customs).
Gautam MachirajuIncoming 1st year, Biomedical Informatics
Mallick Lab
Gautam is an incoming Ph.D. Student in theBiomedical Informatics program after receiving
his B.A. in Applied Mathematics from Universityof California, Berkeley. Under the mentorship of
Dr. Parag Mallick, he currently works onmathematical models of biomarker shedding
kinetics in early-stage tumors, NLP of PubMedbiomarker dark data, and deep learning of
multi-omic time-series patient profiles. He enjoysBay Area events, camping trips, and traveling on
a budget.
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Organizer Remarks
We are proud to host and have you here at the 18th annual symposium for Biomed-ical Computation at Stanford (BCATS). Every year, members of the organizingcommittee and our generous sponsors provide a platform for scientific interactionbetween students, faculty and members of the industry involved in solving compu-tational problems in biology, biomedicine, and healthcare. In the past, our affiliatesand attendees have been involved in some of the most cutting edge discoveries andtechnologies that continue to drive great breakthroughs in these fields and beyond.This year, our participants include students and faculty from Stanford University,UC San Francisco, UC Berkeley, UC Los Angeles, UC Santa Cruz, and Universityof Washington. Our keynote speakers will be speaking on topics such as Person-alized Medicine, Systems Regulomics, and Population & Statistical Genetics, withoverarching themes in Data Mining, Machine Learning and computational methodsdevelopment. Our industry panel includes esteemed speakers from a mix of the BayArea’s dynamic startups and biotech giants including 3T Biosciences, Cardinal An-alytx Solutions, AncestryDNA, and IBM. We are generously supported by variousdepartments within Stanford, the Li Ka Shing Center for Learning and Knowledgeand also our industry affiliates in the Bay Area.
Your organizing committee,
Nicole Ferraro, Lawrence Bai, Irene Li, Gautam Machiraju, Samantha Piekos, YosukeTanigawa
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Keynote Speakers
Nathan Price, PhDProfessor & Associate Director@ Institute of Systems BiologyAffiliate Faculty, Departments of Bioengineering, Computer Science &
Engineering, and Molecular & Cellular Biology
@ University of Washington
Talk title: Mining personal, dense, dynamic data clouds toenhance health and drive discovery
Dr. Nathan Price’s group leverages systems biology to make fundamental contribu-tions to human health. Focusing on the data-driven processes of wellness optimiza-tion, treatment development, and diagnosis precision, the group has pioneered manyunique approaches to analyzing clinical data to optimize therapeutic and diagnosticinterventions. Central to these goals are 1) the 100K Wellness Project, which aimsto detail quantifiable metrics of wellness via analysis of longitudinal clinical data, 2)refining Systems Medicine models to search for diagnostic and therapeutic targets,and 3) integrating biochemical network models into unified computational pipelinesto further streamline genotype-to-phenotype associations.
Jason Ernst, PhDAssistant Professor, Departments of Biological Chemistryand Computer Science@ University of California, Los AngelesTalk title: Computational approaches for interpreting theepigenome and non-coding genome
Dr. Jason Ernst joined the faculty at UCLA in the De-partment of Biological Chemistry, the Computer ScienceDepartment, and the Bioinformatics Program in 2012. His lab is interested indeveloping and applying computational methods, in particular machine learningmethods, for the analysis of high-throughput experimental data to address prob-lems in epigenomics and gene regulation. A primary interest of his is developingcomputational approaches to use epigenomic and other high-throughput datasetsto better understand the non-coding portions of the human genome and its role indisease. Dr. Ernst pioneered computational approaches to learn chromatin statesfrom genome-wide maps of multiple epigenetic marks to systematically annotate thehuman genome. His group’s research is often conducted in close collaboration withexperimental groups.
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Priya Moorjani, PhDAssistant Professor, Department of Molecular & Cell Biol-ogy, Center for Computational Biology@ University of California, BerkeleyTalk title: Genetic insights into South Asian population his-tory and disease
Recently arriving to UC Berkeley in 2018, the Moorjani Labfocuses on using statistical and computational approachesto study questions in human genetics and evolutionary bi-
ology. A central aim in the lab is to understand the impact of evolutionary historyon genetic variation and to apply this knowledge to learn about human history andbiology. They use genetic data from ancient specimens and present-day humans andprimates to learn about: (1) how different evolutionary processes such as mutationrate evolve across primates, (2) when key events (such as introgression and adapta-tions) occurred in human history, and (3) how to leverage these patterns to identifygenetic variants related to human adaptation and disease. The research in the labinvolves both development of new methods and large-scale genomic data analysis.
Ryan Hernandez, PhDAssociate Professor, Department of Bioengineering & Ther-apeutic Sciences@ University of California, San FranciscoTalk title: How evolutionary forces shape the genetic archi-tecture of complex traits
Dr. Ryan Hernandez’ lab uses detailed simulations and pop-ulation genetic modeling to understand the role that natu-ral selection and demography have had on the patterning ofvariation throughout our genomes. His lab develops novelpopulation genetic simulation techniques in order to unravel and interpret thesecomplex evolutionary patterns. Finally, the Hernandez Lab seeks to exploit popula-tion genetic models of demographic history and natural selection to interrogate thegenetic basis of disease. By capitalizing on recent theoretical advances, the groupbuilds models of population dynamics that will utilize genomic re-sequencing datato discover novel regions of the genome that underlie genetic susceptibility to diseaseand drug response.
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Student Speakers
Emily FlynnMeta-analysis of sex-differential gene expression in human liver
Erika BongenKLRD1 expressing NK cells may protect against influenza infection
Pratheepa JeganathanThe block bootstrap method for longitudinal microbiome data
Boxiang LiuGenetic regulatory mechanisms of smooth muscle cells map to coronary artery dis-ease risk loci
Winn HaynesGene annotation bias impedes biomedical research
David GokhmanReconstructing Denisovan anatomy using DNA methylation maps
Industry Panel
Marvin Gee, PhDVP of Research - Target Discovery @ 3T Biosciences
Eurie Hong, PhDSenior Director, Genomics @ AncestryDNA
Natalie Telis, PhDStatistical Geneticist @ AncestryDNA
Brian Maples, PhDVP of Data Science @ Cardinal Analytx Solutions
Joe Davis, PhDData Scientist @ Cardinal Analytx Solutions
Ban Kawas, PhDResearch Scientist @ IBM
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Poster Titles
Alborz BejnoodGenomic and leukocytic inferences of the tumor microenvironment in the context ofnode-negative and node-positive disease
Joshua Bloomstein, Rie von Eyben, and Elizabeth KiddIdentifying a predictive gene expression signature for lymph node involvement incervical cancers
Bryan BunningAge prediction using plasma global metabolic profiles
Claire DonnatInferring microbiome networks
Noah DoveAscribing an etiology to a mutation signature through logistic regression of cancergenomic RNA expression data
Nicholas DworkAutomatically detecting disease markers with optical coherence tomography
Michael GloudemansUncovering tissue-specific mediators of disease-causing genotypes
Charles LiFlexible record linkage tools for data integration of Chinese electronic health records
Greg McInnesPhenotype prediction using a vectorized representation of genomic variants
Aditya RaoA novel multi-cohort framework for analysis of host response signatures
Roger VoldenR2C2: increasing accuracy of MinION sequencing reads
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Li XiaLinked-read, whole genome sequencing reveals pervasive chromosomal-level insta-bility and novel rearrangements in brain metastases from colorectal cancer
Zheng YanAssessing the effects of non-heritable factors on immunological phenotypes
Leeat Yankielowicz-KerenCharacterizing heterogeneity in the tumor immune microenvironment in triple neg-ative breast cancer by multiplexed imaging
Junjie ZhuFacile generation of single-cell transcriptome and immune repertoire from clinicaltumor specimens
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Bio-X is Stanford’s pioneering initiative in the interdisciplinary movement at Stanford
University. Over the past 18 years, Bio-X has developed into an impactful institute that brings together biomedical and life science researchers, clinicians, engineers, physicists, and computational scientists to unlock the secrets of the human body. Over 800 Stanford faculty from all 7 Stanford schools and 65+ departments are affiliated with Bio-X,
and participating in the following Core Programs: Interdisciplinary Initiatives Seed Grant
Program (IIP) Ventures Graduate Student Fellowships and
Bio-X Stanford Interdisciplinary Graduate Fellowships
Undergraduate Research Awards Travel Awards
In addition, Bio-X establishes numerous collaborations between the Stanford scientists and large corporations
by being a networking portal and providing opportunities for companies to join and participate in
symposia/seminars/mixers and customized technical summits, developing faculty liaisons, and more.
The James H. Clark Center is the hub of Bio-X, comprising the equipment, resources, and utilities required to conduct breakthrough research at the cutting edge of engineering, science, and medicine.
STANFORD BIO-X
To learn more about Bio-X, visit our website:
biox.stanford.edu
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Stanford BiomedicalInformatics
TrainingProgram TheBiomedicalInformaticsTrainingProgram(BMI)isaninterdisciplinarygraduateandpostdoctoraltrainingprogram,partoftheBiosciencesProgramatStanfordUniversity’sSchoolofMedicine.WeofferMSandPhDdegrees,andothercourseworkandresearchoptions.
Full-TimeGraduatePrograms: •PhDinBiomedicalInformatics •ResearchMSdegree(primarily,butnotexclusively,forthosewithPhDand/orMD)
Part-TimeDistanceEducationPrograms: •Professional/HonorsCooperativeProgramMSdegree•CertificateinBiomedicalInformatics•Non-degreeoptionforindividualclasses
ForStanfordStudents:•CoterminalMSdegreeinBiomedicalInformaticsinadditiontoBA/BS •PhDMinorinBiomedicalInformaticsforStanfordgraduatestudents
ForStanfordMedicalStudents: •CourseworkandresearchopportunitiesthroughScholarlyConcentrationandMedicalScholarsprograms
AlldegreeprogramsrequirerigorouscourseworkinBiomedicalInformaticscorecourses,acoherentsetofelectivesfromComputerScience,Statistics,Mathand/orandEngineering,andtraininginSocial,LegalandEthicalissues.
Formoreinformation,contact:StudentServicesOfficer StanfordBiomedicalInformaticsTrainingProgram Phone:(650)723-1398MedicalSchoolOfficeBuilding,RoomX-343 email:bmi-contact@lists.stanford.edu1265WelchRoad,MailCode:5464 http://bmi.stanford.edu
Stanford,CA94305-5464
SupportedbyNationalLibraryofMedicineTrainingGrantLM007033
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We aim to understand how the brain gives rise to mental life and behavior, both in health and in disease. Our research community draws from and informs multiple disciplines, including neuroscience, medicine, engineering, psychology, education and law.
The Neurosciences Institute is shaping the future of neuroscience in three interdisciplinary areas:
Stanford Neurosciences Institute
Big Idea NeuroChoice, Understanding and treating addicitve behavior from circuits to policy.
Big Idea Stanford NeuroTechnology Initiative, Creates an incubator for next-generation neural interface platforms.
Big Idea Brain Rejuvenation, Neurodegeneration research focusing on brain maintenance and regeneration, and the role of the immune system in these processes.
NeuroDiscovery - Question-driven discovery about how the brain works
NeuroEngineering - Tools for making novel measurements of brain structure and function
NeuroHealth - Translating neuroscience discoveries into treatments
Boxuan Zhao focuses on the development of multiple molecular tools for transcriptome and connectome studies in neuronal systems.
Sergey Stavisky is developing technology to allow people with paralysis to accurately and intuitively move robotic arms with their minds.
Laura Marquardt’s focus is on improving cell transplantation therapies after spinal cord injury using novel biomaterial design approaches in order to improve functional regeneration.
OpportunitiesInterdisciplinary ResearchBig Ideas in NeuroscienceSeed GrantsVisiting Scholars
TrainingInterdisciplinary Postdoctoral- Scholar AwardsStanford Interdisciplinary Graduate FellowshipsSoftware Carpentry WorkshopsUndergraduate Society - coming soon
Engaging our CommunityWeekly Seminar SeriesAnnual SymposiumRetreatBrain Broadcast Newsletter
Get Involvedhttp://neuroscience.stanford.edu
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For more information, please visit ccsb.stanford.edu
How To Get Involved • CCSB 6th Annual Symposium
o May 11, 2018 – LKSC Berg Hall o Submit and abstract to be part of our poster
session or to be selected for a speaker slot o Register Today:
ccsb.stanford.edu/events/symposium/symposium2018.html
• CCSB Monthly Seminars o Subarna Sinha, SRI International, 4/27, 12:30pm – Clark S360 o Rahul Satija, New York University, 5/18, 11:00am – Clark S360 o Doug Lauffenburger, MIT, 5/22, – Clark S360 o Zena Werb, UCSF, 6/8, – Clark S360 o Additional seminar information at:
ccsb.stanford.edu/events/seminars/2018-seminars.html
• Cancer Systems Biology Scholars (CSBS) Program o Fellowship Opportunity: med.stanford.edu/csbs/news.html o CSBS Journal Club: med.stanford.edu/csbs/events/journalclubs.html
• Join our mailing lists to stay up-to-date with the latest news and event
o ccsb-announcements@lists.stanford.edu o csbs-journalclub@lists.stanford.edu
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Stanford Cancer Institute
LEADING THE WAY CANCER IS TREATED TODAY AND TOMORROW
The Stanford Cancer Institute (SCI) is committed to giving patients every clinical and technological advantage in the pre vention and treatment of cancer. The SCI leverages the expertise of over 300 physicians and researchers working together to unravel cancer’s secrets. Stanford’s scientific focus includes cancer cell and stem cell biology, immunology, molecular imaging and genetics. Translational medicine is the cornerstone of Stanford’s cancer treatment programs, combining new advances with compas sionate care and supportive services.
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Stanford’s Center for Computational, Evolutionary and Human Genomics
Founded in 2012, CEHG supports and showcases the cutting edge scientific research conducted by faculty and trainees in more than 40 member labs across the School of Humanities and Sciences and the School of Medicine. CEHG members collaborate on interdisciplinary research projects at the forefront of the information age of genomics in order to improve human well-‐being.
Trainee Fellowships: • Fellowship support is centered on the transition from graduate school to
postdoctoral fellowship. • Fellows receive: financial support during the transition period; conference
travel support; opportunities to lead and participate in Center scientific activities; and feature blog interviews.
Symposia and Seminars: • Annual symposium features faculty and trainee research from member labs
and guest keynote/faculty speakers from the Bay Area and beyond. • Evolgenome seminar series explores Stanford and guest faculty/trainee
speaker research on CEHG topics. Meets 2-‐3 times a month on Wednesdays, during the lunch hour. Food is provided.
Science Education Outreach:
• Curriculum support for lessons in science and genetics, and panel presentations on STEM education and professions, for local middle-‐ and high-‐ school classrooms.
• Coordinated science lab tours for visiting student groups; and trainee-‐led education outreach events.
Event and Program Partnerships:
• 2018 Event partnerships include the Tinker Symposium on Latin American Research in Biodiversity (2/27), and BCATS 2018 (4/19).
For more information, contact: Katie M. Kanagawa, Ph.D. CEHG Program Manager Phone: (971)570-‐0998 Littlefield Center, Room 315 Email: stanfordcehg@stanford.edu 365 Lasuen Street, Mail Code: 2069 https://cehg.stanford.edu/
Stanford, CA 94305-‐5464
CEHG
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Thank You
Monica James
Joan Menees
Ayla Akgul
Linny Le
Joy Morimoto
LKSC staff
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